It is now recognised that shallow and eutrophic freshwater lakes have two possible alternative photoautotrophic dominant states: (1) domination by submerged vegetation and (2) domination by phytoplankton. The suggested mechanism(s) of alternation between these polar states is an intricate function of stochastic trophic disturbance allied to underlying changes in the bioavailability of nitrogen and phosphorus. Despite a clear conceptual appreciation of the mechanism of state alternation, concerted research on defining the spatial and temporal nature of the interrelationship between photoautotrophic community dynamics and the environmental controls that regulate state alternation has been limited. A fuller understanding of the diurnal and seasonal variability of the phytoplankton community and the possible impacts for aquatic vegetation arising from bloom development needs to be sought. However, delineating spatial and temporal patterns in community ecology through single-point sampling methods is generally problematic. Phytoplankton and aquatic vegetation communities are typically heterogeneous in terms of distribution, composition and condition which, when allied to the inherently transient nature of aquatic systems, makes the acquisition of representative spatiotemporal data from in situ sampling campaigns unfeasible. Remote sensing can, however, provide an effective synoptic and multitemporal characterisation of environmental phenomena at a range of spatial scales. Potentially, remote sensing may be able to provide an improved insight into photoautotrophic response to changing environmental controls in shallow lakes.