Marine Protected Areas (MPAs) have been promoted as effective management tools to protect biodiversity at local and global scales, but there remains considerable scientific uncertainty about effects of MPAs on species abundances and biodiversity. Commonly used assessment designs typically fail to provide irrefutable evidence of positive effects. In contrast, Before-After-Control-Impact (BACI) designs potentially remedy many of these problems by explicitly dealing with both spatial and temporal variation. Here, we document the historical context of implementation and the scientific assessment of MPAs recently established at eight sites around the island of Moorea, French Polynesia. In 2004, we designed and implemented a monitoring plan that uses a BACI-Paired Series (BACIPS) design to quantify the effect of the MPAs. Twice per year, we monitor fish, corals, and other benthic invertebrates at 13 sites (eight within MPAs and five outside MPAs) around Moorea, in three distinct reef habitats (fringing, barrier reef, and outer slope). We present statistical analyses of data collected during five surveys (July 2004 to July 2006), before the initiation of enforcement. We also assessed the potential of our program to detect future responses to the established MPA network. Our estimates of biomass for five categories of fishes (Acanthuridae, Chaetodontidae, Serranidae, Scaridae, and fisheries target species) within MPA sites generally track estimates in paired Control sites through time. Estimated statistical power to detect MPA effects (a 192% biomass increase within the MPA) was high at the MPA network scale but varied among taxonomic categories and reef habitats: power was high on the reef outer slope and lower in the lagoon, and generally high for acanthurids and chaetodontids. It did not vary significantly between sites. We discuss limitations of our approach (shared by all MPA assessments to date) and describe solutions and unique opportunities to redress these limitations in French Polynesia.