For species' dynamics highly influenced by environmental conditions, sustainable management for conservation and/or exploitation purposes requires the ability to segregate natural processes from anthropogenic impacts. In this context, identification of phenotypic variations in morphological patterns, and clarification of the mechanisms involved, constitute useful tools to identify adequate management measures from Europe-wide to local conditions. Although such approaches are already used effectively in the management of fish stocks, they are more recent for bivalve stocks, which are also good candidates for such management tools. The current study examines morphological patterns in the Manila clam (Venerupis philippinarum) through morphometric studies of 4 populations on the French Atlantic coast (Banc du Guer, Morbihan Gulf, Bellevue, and Arcachon Bay). The methodology relies mainly on conventional shape analysis using 8 morphometric ratios involving metrics and weight. In addition, an outline description was created for selected individuals that revealed different forms of the anterior—dorsal valve margin identified for future research. Using supervised classification methods, morphometric—latitudinal trends were revealed between northern and southern populations of V. philippinarum. Relationships between discriminatory morphometric ratios (describing elongation, valve density, and weight related to length) and available environmental conditions (temperature, salinity, and chlorophyll a concentrations) were considered using linear multilevel models. They revealed significant relationships with chlorophyll a concentrations and with 1 ratio with seawater temperature ranging from 12–20°C. Four potential causes were hypothesized to explain the unexpected relationship identified between morphometric characteristics and trophic conditions: (1) a negative effect resulting from high chlorophyll a concentrations, (2) a masked effect of other food resources affecting valve growth, (3) interspecific competition for food among filter-feeding populations, (4) and effects of other environmental parameters such as sediment type. Observed differences in shape may result from a combination of these 4 causes with varying degrees, depending on site-specific environmental conditions. Last, the consequences of morphometric variation on population regulation are addressed.