Comparison between two similar ecosystems, different in size, in terms of organism population requires that differences in parameters be analyzed carefully. The parameters that may have a significant effect on organism population include environmental factors, food availability, predation, competition for resources, etc. We can also classify these factors as abiotic and biotic. Assuming all the environmental factors (including temperature, pressure, humidity, oxygen concentration, etc.) are same between the lakes, any of the other factors maybe responsible for similar population levels. Similar levels simply means that the larger lake has lower concentration of organisms. The larger lake may have more predators thus keeping the population concentration low or there may be more competition for the food (it is not clear if the similar levels of population also mean similar species; all the organisms could be from one or two species, thus increasing the competition).
Also, it is not clear if there is geometric similarity between the lakes, a deeper lake may become larger (and have same surface area as the smaller lake; even lesser area is also possible). In such a scenario, the deeper lake will have lesser organisms at greater depth (due to lower oxygen concentration), thus overall may have similar population as smaller lake.
So, without further information and clarity, we can theorize that predation or lack of enough food (or competition for resources) may cause a larger lake to have similar population levels as a smaller lake.
Hope this helps.