In the present work, the relative effects of the season (early vs. late summer), site (Gulf vs. Pacific study sites), the population of origin (Gulf vs. Pacific) and associated abiotic variables were determined in two geographically-separated Nodipecten subnodosus populations and their reciprocal transplants, through the scope for growth (SFG) and net growth efficiency (K2) using a portable open-flow system. Results indicate that both energy acquisition and expenditure were significantly affected by season, site, and population factors. Scallop energy acquisition and growth efficiency were highest during the earlier, cooler part of the summer and higher at the Pacific site where food availability was highest. Significantly higher respiration rates were measured for the Pacific scallop population, leading to significantly lower net growth efficiency than scallops of Gulf origin, which indicates a physiological advantage for Gulf scallops during the suboptimal growth conditions present during summer months on both coasts of the Baja California peninsula. It may have important implications for aquaculture enterprises in this region, and may also confirm the genetic divergence between these two geographically separated populations. The advantages of the open-flow system for in situ ecophysiological studies in aquatic organisms are discussed.