Giant clams are endangered in many parts of their Indo-Pacific range owing to adult specific overharvesting that threatens recruitment, a demographic parameter exhibiting high sensitivity to environmental disturbances and adult densities among tridacnids. Lakshadweep reefs are not subjected to commercial giant clam fishery, and population assessment has not been carried out in these waters so far. We monitored the small giant clam Tridacna maxima populations in confined waters of 12 reefs in Lakshadweep Archipelago during 2005–2007 using a systematic line transect based distance sampling framework. Overall T. maxima density in the Archipelago was estimated at 141.2/ha (95% CL 118.2–168.7) in 2005 and 122.7/ha (103.60–145.37) in 2006. Populations showed wide variation in densities and relative proportions of different age-classes between reefs. While Agatti, Bitra and Chetlat lagoons harboured high clam densities, Amini harboured the most impoverished population. Data simulation showed that total clam count along transects of 100 m length × 2–5 m strip width, in a minimum of 140 replicates, stratified by area among lagoons, would provide a viable monitoring index for rapid assessments of T. maxima in Lakshadweep. Compared to unbiased absolute abundance estimates, this monitoring index could be achieved more easily, without much compromise on accuracy and precision, necessary for meaningful spatio-temporal comparisons.