Obviously, chemical fertilizers are a problem as pollutants go, since they skew the resource constraints that operate in rivers, lakes, streams, and the ocean- those chemicals effectively fertilize algae in the water, which then proceeds (through the death and decomposition of that same algae and blocking sunlight from reaching the deeper parts of the water column) to reduce the available oxygen. This water pollution has a direct and deleterious effect on aquatic ecosystems.
Pesticides, herbicides, and industrial waste present their own complications. Industrial and agricultural operations are the largest consumers of water and the most likely to generate waste. While some chemicals (such as DDT, a compound that was responsible for thinning the eggshells of many avian species and endangering the well being of the bald eagle and California condor) are widely recognized to be dangerous to organisms, many human-generated compounds have not been studied for deleterious effects on the environment, and, as mentioned before, it’s extremely difficult to decontaminate groundwater once it becomes polluted. Since a large fraction of our waste ends up in landfills, how they cope with the chemicals that end up in them and the water that falls on them can improve or worsen water quality in their communities. Even airborne pollutants can be an issue for aquatic ecosystems, as is shown by this study!
In addition, sand and sediment can be a pollutant, as can heat, since all of them can make it more difficult to get the light or oxygen required or make it impossible to breathe. All species have a range of conditions that they can tolerate; some have far narrower restrictions than others- for instance, trout require a lot of dissolved oxygen, which in turn requires colder waters (since water temperature and the maximum amount of dissolved oxygen are inversely related). Given the limited mobility of many freshwater aquatic species (especially macroinvertebrates), these “non-lethal pollutants” are significant dangers. Removal of riparian corridors (vegetated areas adjacent to waterways) both increases the temperature of those waterways, reducing the maximum amount of dissolved oxygen that they can carry, and increases the incidence of runoff- and erosion-related pollution.