Based on instream habitat characteristics, sections of streams and rivers can be divided into three major categories (Table 1). Pools and runs are typically associated with feeding lanes for trout, whereas riffles provide very good habitat for a large and diverse number of aquatic insect species.
| Table 1: Three major habitat characteristics of a stream or river. | |
| Habitat Characteristic | Description |
| Pool | Portions of the stream with reduced current velocity at low flow and with deeper water than the surrounding area. |
| Riffle | Shallow rapids where the water flows swiftly over completely or partially submerged materials to produce surface agitation. |
| Run | Areas of swiftly flowing water, without surface waves, which approximates uniform flow, and in which, the slope of water surface is roughly parallel to the overall gradient of the reach. |
The flow of water in a stream is typically unidirectional, from upstream to downstream. There are however, some minor exceptions such as the upstream movement of water in the backwash of some pools. Due to the body design of a trout, they are unable to hold position while oriented downstream, with the flow. Therefore, trout hold their position while facing into the flow.
Within the water column, there is a gradient of current velocity where the water current is generally faster at the surface and slowest at the bottom of the stream (Figure 1). At the surface, water encounters little friction with air; however, as you move down into the water column friction increases. The current velocity gradient is exaggerated with depth, where increased depth results in decreased current velocity. At the substrate surface, water velocity is the slowest in an location called the boundary layer. This boundary layer is an area where a sharp decrease in water velocity results from increased friction with the substrate surface. This area can extend up to 4 mm above the surface of stones and debris on the bottom of a stream or river.

Figure 1: Simplified current velocity gradient within the water column. The large, dark blue line near the surface represents increased current velocity. The shorter, light blue lines represent reduced current velocity approaching the bottom of the stream or river. Side view.
Current velocity and water flow patterns within a stream or river is complicated when instream obstacles are present (Figures 2 and 3). The change in current velocity and water flow around a single stone illustrates that there is tremendous variation in even the most uniform natural stream.

Figure 2: Looking down at water movement around a single obstacle.

Figure 3: Simplified view of water movement around a single obstacle. Side view.
A trout can conserve energy by positioning itself in holding water, that is, either behind or directly in front of instream obstructions such as vegetation, stones, logs, and rot wads. Trout often stay in the holding water created by these instream obstructions and will leave only when it is to their advantage. For example, trout will leave holding water when they are chased or they are feeding. In fact, trout readily leave holding water to capture food that is "funnelled" around an obstruction. The increased concentration of food items around an obstruction, combined with a trout's conservation of energy while in the holding water, creates an effective feeding lane. Typically, trout will accelerate into the funnelled water of the feeding lane after food items. Once the food is captured, or missed, the trout will let the current swing it around so it can return to its original position in the holding water section of the feeding lane.
Deep water, under-cut banks and overhanging vegetation can provide protection (cover) from predators such as birds and anglers. Insects (aquatic and terrestrial) also live around and on stream and bank structures, so food is readily available for the trout.
Upper reaches of a stream or river, such as headwater and foothill regions are generally cool, shallow and fast. This is because upper reaches are usually narrow channels with increased bank cover and a steep gradient. As you proceed downstream, channel width increases so less of the stream is shaded by streamside vegetation, and the stream gradient decreases. These factors result, in part, to lower reaches generally being warmer, deeper and slower.
Regardless of relative location along a stream or river system, either headwater or lower reaches, temperature varies both daily and seasonally (Figures 4, 5, and 6). As daily air temperature changes so does water temperature. There is however, a lag time associated with the change in water temperature. This is due to one of the many properties of water - its ability to retain and resist temperature change. On a typical day in May, air temperature will peak around 2:00 p.m., but water temperature will peak around 4:00 p.m. As day-length increases, peak air and water temperature will occur later. For example, in August, air temperature will peak around 4:30 p.m. and water temperature will peak around 6:30 p.m. Water temperature will also vary with depth. Surface water will generally be closer to air temperature, whereas deeper water tends to stay cooler, especially if there is groundwater input.

Figure 4: An example of daily temperature ( C) fluctuations from May 5 to 25 in a typical mountain or foothill stream. Temperatures were collected near the stream bottom with a continuously recording thermograph.

Figure 5: An example of monthly temperature fluctuations ( C), over two years, in a typical mountain or foothill stream.

Figure 6: Peak water temperature ( C) for six consecutive days in August, within a typical mountain or foothill stream. Each line represents a single day.