Juvenile mussels enter the benthos after excysting from a fish host and settling to the bottom where they inhabit the interstitial zone in rivers. We examined the algal composition in the surface water and pore waters in different locations in a temperate river (Thames River) in Southern Ontario. Surprisingly, algal concentration (C) was~9× higher in pore water versus surface water and varied spatially in the riverbed (downstream of boulders > upstream of boulders and nonbedform regions), and pennate diatoms were the most abundant taxon in the pore waters. We examined the clearance rate (CR; mass of suspended material removed from the water per unit time and mussel) of recently metamorphosed juvenile unionid mussels (3-to 4-week-old Lampsilis siliquoidea, Fatmuckets) exposed to pore water and surface water in a paddle wheel flow chamber at different water velocities (U). Juvenile CR based on Chlorophyll a fluorescence was~2× higher on pore water versus surface water and CR based on a specific algal taxon, identified via flow cytometry, varied with its initial concentration. Chesson's feeding electivity index revealed that mussels removed five chlorophyte taxa in proportion to their concentration in the water (i.e., removed at random), but they removed five diatom taxa in greater proportion (i.e., selected for by juvenile mussels) across the range of algal flux (J = UC) examined. This study provides evidence of the importance of diatoms in pore waters to juvenile mussels. It also reveals elements of the physicochemical environment used by juvenile mussels, which should be considered in their conservation.Plain Language Summary Native freshwater mussels are called ecosystem engineers because of their profound influence on water quality, nutrient cycling, and food webs. Juvenile mussels live in the bottom of rivers where they rely on flow within the riverbed (pore water flow) to supply them with algal food and oxygen needed to live. These materials are carried in rivers primarily via water that enters the riverbed in locations such as upstream of boulders; it leaves at other locations, for example, downstream of boulders. We examined the algal composition of the river both in the surface and in the pore water over the summer. Surprisingly, there was much higher algal concentration in the pore water. Juvenile mussels fed at twice the rate on pore waters, and they preferred diatoms (algae that make glass cases and are very productive) over other algae. This was likely because of the high nutritional quality of diatoms. Unfortunately, we also found that the riverbed environment suffered from low oxygen levels and high ammonia levels in the summer, which could be lethal to juvenile mussels. Human-caused changes to environmental conditions that reduce pore water flow and water quality and/or the types of algae present in riverbed could limit the survival and growth of juvenile mussels.