4.1. Fish
Typhoons caused landslides and debris flow that decreased fish populations [
10]. The abundance of
H. formosanus and
O. alticorpus decreased after typhoons (
Table 1). Additionally, the length and weight of
R. nantaiensis and
O. alticorpus decreased at both stations after typhoons. The habitat types in the study area had been transformed into shallow riffles or runs by channel dredging and following-up sediment accumulation after typhoons [
45].
H. formosanus preferred shallow water, which was expected to provide them with better refuge and food sources [
34,
46]. However, debris flow and landslides caused serious fatality of the fish species [
4,
10,
12,
28,
29]. The abundance of
R. nantaiensis slightly increased at both stations after typhoons, but the length and wet weight of
R. nantaiensis decreased at the two stations (
Table 1). Typhoon Morakot was a serious disturbance to the environments, so the habitats and organisms (fish and invertebrates) perhaps had not fully recovered in Cishan Stream. Fish fauna recovered to a pre-typhoon condition 14 months after Typhoon Herb in Cishan Stream [
12], but the disturbance of Typhoon Morakot was greater than the disturbance of Typhoon Herb.
R. nantaiensis prefers the substrate composition of gravel and pebbles [
46]. In this study, the substrate environment almost changed from boulders and cobble to pebbles, gravel, and sand at both stations after typhoons (
Table 2), making them more suitable for
R. nantaiensis. In contrast,
O. alticorpus prefers boulders [
45], so their numbers have decreased due to the environmental change caused by typhoons. Finally, fewer adults of
O. alticorpus were found in the study area.
4.2. Microhabitat
Stream habitats were destroyed by debris flow and landslides caused by typhoons [
12]. Water temperature was higher after typhoons than before typhoons (
Table 2). This was because the pre-typhoon samples were concentrated during the winter and spring when air temperatures were cooler. After typhoons, EC and turbidity were higher than before typhoons (
Table 2) because riverbanks had been weakened, allowing for soil and sands to be eroded into the river. Furthermore, the upstream segments of the river were still undergoing construction to repair typhoon damage. This could further contribute to the increased turbidity and EC values. DO was lower after typhoons (
Table 2) because the majority of the macrophytes, algae, and microorganisms were covered by the amount of sediments, decreasing the oxygen content [
25]. Salinity and pH were the only characteristics that showed little difference before and after typhoons.
After typhoons, dredging was used in the stream to form a deep and narrow straightened main channel based on human safety and local structure. However, the channel after dredging resulted in the homogenization of stream habitats that affect habitat availability for aquatic organisms [
57]. The results show that the mean flow velocity and mean water depth were generally higher before typhoons, with the exception of mean flow velocity at Min-Chuan Bridge (
Table 2). Furthermore, the standard deviation of flow velocity and water depth were both higher before typhoons. It indicates that the flow velocity and water depth were more diverse before typhoons than after typhoons. Diverse habitat environments had a positive correlation with biodiversity [
45,
58,
59].
4.3. Critical Habitat Requirements
Critical habitat requirements try to show that these environmental factors were critical to fish in survival after serious disturbances. They need to be kept similar no matter how the stream habitat environment has been changed. Water depth and pebbles were not significantly different before and after typhoons (
Table 3). This illustrates that water depth and pebbles were critical to the survival of adults of
H. formosanus after typhoons. Therefore, water depth and pebbles were critical habitat requirements for the adults of
H. formosanus. In contrast, all factors were significantly different for the juveniles of
H. formosanus, meaning that no factors were critical habitat requirements (
Table 3). Sand, water depth, and pebbles were not significantly different for the adults of
R. nantaiensis, so water depth, sand, and pebbles were critical to the adults of
R. nantaiensis in survival after typhoons (
Table 4). The result for the juveniles of
R. nantaiensis was the same as for
H. formosanus, meaning that there were no factors that were critical habitat requirements (
Table 4). Chiu and Suen [
45] used principal component analysis to examine the relationships between four fish species and thirteen environmental factors in the Cishan Stream, and they found that
H. formosanus and
R. nantaiensis had a noticeable correlation to water depth. Furthermore,
H. formosanus preferred pebbles [
45,
46], and
R. nantaiensis preferred pebbles and cobbles but avoided boulders [
46]. Consequently, it is important to maintain water depth and substrate types for the adults of
H. formosanus and
R. nantaiensis after serious disturbances.
Flow velocity and the standard deviation of flow velocity were not significantly different for the juveniles of
O. alticorpus (
Table 5) before and after typhoons. Lyu and Suen [
39] confirmed that
O. alticorpus can adapt to less than 1.05 m/s when considering all life stages. In this study, the flow velocities were 0.57 m/s and 0.48 m/s before and after typhoons, respectively. Consequently, the flow velocity and variability of flow velocity were critical habitat requirements for the juveniles of
O. alticorpus.
4.4. Tolerable Habitat Requirements
Tolerable habitat requirements describe environmental factors for which fish can tolerate some variation. EC, turbidity, DO, standard deviation of water depth, sand, and boulders were tolerable habitat requirements for the adults of
H. formosanus. Before typhoons, the adults of
H. formosanus preferred a habitat with a high DO, but they did not exhibit any preference after typhoons (
Table 6). The higher turbidity could lead to a decline in plankton [
60], which produced low oxygen content [
25]. However, the adults of
H. formosanus reflected no correlation with DO after typhoons (
Table 6). This suggests that this variation could be tolerable for the adults of
H. formosanus. EC, the standard deviation of water depth, sand, and boulders were significantly different for the adults of
H. formosanus (
Table 3). However, the adults of
H. formosanus reflected no correlation with EC, the standard deviation of water depth, sand, and boulders during pre-typhoon and post-typhoon periods, respectively (
Table 6). Consequently, the variation in EC, standard deviation of water depth, sand, and boulders could be tolerable ranges for the adults of
H. formosanus.
Tolerable habitat requirements, which include turbidity, the standard deviation of flow velocity, gravel, pebbles, and cobble for the juveniles of
H. formosanus, were different from the requirements for adults. Although turbidity and the standard deviation of flow velocity had great changes after typhoons (
Table 3), they did not affect fish preference before and after typhoons (
Table 6). Before typhoons, the juveniles of
H. formosanus preferred habitats with pebbles; there is no similar preference for the substrate composition of pebbles after typhoons (
Table 6). This suggests that the juveniles of
H. formosanus could tolerate such variations.
H. formosanus avoids sandy substrate [
46], so the variation of gravel and pebbles could be tolerable ranges for the juveniles of
H. formosanus in this study.
EC, turbidity, flow velocity, standard deviation of flow velocity, gravel, and cobble were tolerable habitat requirements for adults of
R. nantaiensis. After typhoons, EC, turbidity, and gravel increase greatly, and the standard deviation of flow velocity and cobble decrease (
Table 4). However, all of these factors had no correlations with the adults of
R. nantaiensis before and after typhoons, respectively (
Table 7). Flow velocity has no correlation after typhoons, but it had a positive correlation before typhoons (
Table 7).
R. nantaiensis preferred higher velocity [
46], but adults could be tolerable variations of flow velocity after typhoons.
All factors were tolerable habitat requirements for the juveniles of
R. nantaiensis except DO, flow velocity, water depth, and standard deviation of water depth. All of these factors showed marked change after typhoons (
Table 4), but they did not affect the preference of for juveniles (
Table 7).
R. nantaiensis preferred shallow water [
45,
46], but juveniles of
R. nantaiensis had a negative correlation with water depth in this study after typhoons (
Table 7). Juvenile fish had a limited swimming ability and range of motion [
61,
62], so they perhaps avoided too-low water depth to be predated. The abundance of juveniles after typhoons (n = 139) was more than that before typhoons (n = 60) based on sampling data. This suggests that the juveniles had a high tolerance for EC, turbidity, standard deviation of flow velocity, and substrates.
All factors were tolerable habitat requirements for the juveniles of
O. alticorpus. EC, turbidity, DO, sand, gravel, pebbles, and cobbles do not have significant correlations with the juveniles of
O. alticorpus before and after typhoons, respectively (
Table 8). This illustrates that these environmental factors do not affect the fish assemblage during both periods. The water depth, standard deviation of water depth, and boulders had positive correlations before but no correlations after typhoons. This suggests that these environmental factors positively affect fish assemblage before typhoons and do not do so after typhoons.
O. alticorpus preferred deep water [
45,
46], and this study observed similar findings for the juveniles of
O. alticorpus before typhoons. However, although the juveniles had no correlation with water depth after typhoons, they can seemingly adapt to water depth. In this study, the range of water depth is mainly between 30 cm and 40 cm, which proves that juveniles can still adapt to such depths. Juveniles can tolerate the changes in substrates because they can adapt to diverse substrates [
39].
4.5. Applications of Habitat Requirements for Restoration and Ecological Engineering
Habitat changes indeed affect fish assemblages after typhoons [
12], but different environmental factors have different influences. Therefore, an important goal of this study was to provide this information for restoration. The definition of critical and tolerable habitat requirements can help in understanding critical environments and tolerable variability for juveniles and adults. When considering critical habitat requirements, a water depth of 33.16–35.03 cm and substrate with 23.90–32.60% pebbles were critical ranges for the adults of
H. formosanus in survival; a water depth of 22.73–29.62 cm, substrate with 1.50–7.70% sand, and 32.30–46.90% pebbles were critical ranges for the adults of
R. nantaiensis in survival; and a water velocity of 0.48–0.57 m/s with a standard deviation of 0.22–0.25 were critical ranges for the juveniles of
O. alticorpus in survival (
Table 9). This is valuable information for restoration design. Also, different life stages of different species may have different tolerable habitat requirements. This is especially relevant to the juveniles of
O. alticorpus, which is more tolerable of habitat than any other species (
Table 6,
Table 7 and
Table 8). However, the tolerance of
O. alticorpus is still questionable because no adults were caught in this study. Overall, the application of this information to habitat suitability indices or consideration of tolerable habitat ranges in future restoration projects could allow for a better reflection of organisms’ needs.
In summary, this study compares environmental factors and fish assemblage before and after typhoons by exploring the habitat requirements of three dominant species, H. formosanus, R. nantaiensis, and O. alticorpus. Salinity and pH showed few changes, but electrical conductivity, turbidity, dissolved oxygen, water velocity, the standard deviation of water velocity, water depth, standard deviation of water depth, and substrate all showed notable changes after typhoons. The abundance of two dominant species (H. formosanus and O. alticorpus) decreased after typhoons, likely because of the increase in finer particles (sand and gravel) after typhoons. The standard length and wet weight of the collected fish also decreased after typhoons, except for the H. formosanus. Water depth and pebble substrate were critical habitat requirements for the adults of H. formosanus, making these two important factors for the restoration of the species. Water depth, sand, and pebbles were important factors for the adults of R. nantaiensis, while low flow velocity and variability of flow velocity were important factors for the juveniles of O. alticorpus. This critical and tolerable habitat requirement information could provide preferable ranges of environmental factors for restoration to create more suitable habitat environments for aquatic organisms. Our study shows how fish communities change after storms and identifies critical factors that influence fish distribution. It would be very important from a management standpoint to try to minimize impacts from floods and carefully restore streams with some nature-based solutions so that they can provide more suitable habitats for fish.