Phytoplankton assemblages are privileged descriptors of the ecological status of marine ecosystems regularly included in routine monitoring programmes. The high spatial and temporal variability of phytoplankton and the intrinsic difficulties of species identifications, however, combine in making reiterate assessments of this component of marine biota particularly demanding. Coarse levels of taxonomic resolution (e.g., genus, family) or morpho-functional categories have been proposed to reduce identification efforts or to ease the analysis of phytoplankton assemblages for monitoring purposes, although with contrasting outcomes. A major issue is that, in the absence of control for the loss of information associated to these alternative approaches, their application may lead to poor representations of genuine spatial and/or temporal patterns of assemblages in relation to natural and anthropogenic sources of variation. We provided a new approach to reduce the efforts required to analyse phytoplankton assemblages that integrate morpho-functional classification of phytoplankton with the use of null models to estimate the consequent loss of information on species-level community patterns. Null models for information loss were built by randomly grouping the original species variables into a progressively decreasing number of groups, in order to identify the minimum number of aggregate variables needed to detect community patters as at species level. Aggregate variables were then defined as morpho-functional groups, by grouping species on the basis of a combination of morpho-functional traits, including general taxonomy, cell size, shape, elongation and complexity. We applied the approach to six case studies investigating the response of phytoplankton assemblages from marine and transitional water ecosystems under different environmental settings in areas spanning the world’s ocean, including coral atolls, mangroves, estuaries, coastal lagoons and inlets. The approach allowed obtaining parsimonious sets of morpho-functional groups, which were suitable to detect changes in phytoplankton assemblage structure as at species level in all case studies. Trait-based approaches to phytoplankton research and monitoring are crucial to shed light on processes underlying phytoplankton community assembly and dynamics in the face of global change. In this perspective, our framework incorporates cost-effectiveness, instances from traditional monitoring programmes aiming at the detection of community patterns, and the current need for a deeper understanding of functional responses of phytoplankton to environmental drivers.