This chapter provides an analysis of status and trends in ecology, freshwater biodiversity and conservation within natural lakes of Albania using a combination of: (i) quantitative data; (ii) qualitative data from a literature review; and (iii) evidence from the peer-reviewed scientific literature. This contribution considers biodiversity of the Albanian standing freshwaters in the broadest sense, focusing specifically on Prespa, Ohrid and Shkodra Lake ecosystems. During the writing of the chapter, it became apparent that any conclusions drawn from the data would be necessarily limited due to a general lack of quantitative, nationally consistent, observational data for aquatic species and habitats of the large Balkan Lakes. For this reason, proxies, for example habitat trends, have been employed to examine likely trends in biodiversity that is highly affected by anthropogenic activities and climate changes. These trends are also explored further within the context of the eco-region considerations. With this approach, we attempt to explore key trends in lake and other aquatic ecosystems, with coverage of the following areas: (i) native, rare and endemic species at risk; (ii) water oscillations; (iii) habitat loss and fragmentation; (iv) pollution, nutrients, and eutrophication; and (v) future climate implications. Finally, given to that fact large lakes in Albania are part of the protected area system, chapter addresses conservation needs and necessity for building proper resilience.