In recent years, microbial ecology has developed from a peripheral discipline into a central field of microbiology. This change in state and perception is mainly driven by a rapid development of methods applied in the manifold fields related to microbial ecology. In biogeochemistry, for example, the use of high-resolution techniques such as FT-ICR-MS (Fourier transform ion cyclotron mass spectroscopy) has uncovered an enormous diversity and complexity of natural organic matter produced or degraded microbially either in dissolved or particulate forms. On the other hand, the introduction of high-throughput sequencing methods, such as 454 pyrosequencing, in combination with advances in bioinformatics allows for studying the bacterial diversity in natural samples circumventing cultivation dependent approaches. These new molecular tools enable in depth studies on single-cell genomes, distinct populations or even metacommunities. In combination with metatranscriptome and proteome studies it is for the first time possible to simultaneously unravel the structure and function of complex communities in situ. These technique-derived findings have, on the one hand, dramatically increased our knowledge on the vast diversity and complexity of bacterial habitats and, on the other hand, on phylogentic diversity and physiological responses of natural bacterial communities to their environment. However, until now microbial ecology is lacking an ecologically relevant species definition and useful tools for the identification of ecologically coherent taxa. Studies on intra- and interspecies interactions even with higher organisms demonstrate that bacteria can rapidly adapt to temporal and spatial changes in their environment. Aquatic bacteria have optimized and dramatically expanded their living space by efficient exploitation of organic matter point sources such as particles/aggregates and higher organisms. Although it is evident that particles/aggregates and organisms such as phytoplankton are ‘hotspots’ for microbial growth and transformation processes, it has not affected sampling strategies of aquatic microbial ecologists, who often focus solely on the free-living bacterial fractions and a priori exclude higher organisms by non-representative water sampling. Therefore, aquatic microbial ecologists have largely overlooked the fact that many aquatic bacteria may possess a complex lifestyle and frequently alternate between a free-living and a surface-associated stage. Here, I propose that modern concepts in aquatic microbial ecology should take into account the high chemical diversity and spatio-temporal variability of the bacterial environment. Interactions of aquatic bacteria with surfaces including living organisms are the key to understanding their physiological adaptations and population dynamics, as well as their contribution to biogeochemical cycles. New sampling strategies and theoretical concepts are needed in aquatic microbial ecology to access the whole spectrum of bacterial lifestyles and their ecological and evolutionary consequences.