We present an overview of the main physical, chemical and ecological features of lake ecosystems. The main aim is to briefly address the complexity of this subject. The solute composition of lake water depends upon a number of interplaying factors, including the watershed geology, land uses, climate, pollution sources, thermal regime and biota. Excess nutrients (N and P) from diffuse or point sources may trigger eutrophication processes, resulting in algal blooms and oxygen shortage. For this reason, a great wealth of studies has been performed on the causal factors and effects of eutrophication and possible remedial measures. In recent decades, P loadings from point sources decreased due to the enforcement of strong environmental policies, e.g. the implementation of wastewater treatment plants. Nonetheless, the restoration of pristine conditions has not yet been achieved because P may be recycled in large amounts from anoxic sediments, thus providing an internal source. Nitrogen loadings decreased proportionally less, mostly due to land use and diffuse pollution from agriculture and livestock, leading to new and challenging issues, e.g. the combined stoichiometry of N, P and Si as a driving factor of lake productivity and the food web. In the last two decades, studies on dissolved organic carbon have assumed a growing importance. This source of organic carbon fuels microbial communities and heterotrophic activity, with side effects on carbon dioxide emissions. The bulk of dissolved molecules composing this organic pool may also support planktonic production. Finally, they have optical properties, which are largely unexplored for their effects on lake ecology.