The Malta-Comino Channel (Maltese islands, central Mediterranean), supports extensive meadows of the seagrass Posidonia oceanica that in some places extend to a depth of around 43 m, which is rare for this seagrass. To assess spatial and temporal variation in the state of the deeper parts of the P. oceanica meadow with time, data on the structural characteristics of the seagrass meadow at its lower bathymetric limit were collected during the summers of 2001, 2003 and 2004 from four stations (two stations within each of two sites) located at a similar depth, over a spatial extent of 500 m. Shoot density was estimated in situ, while data on plant architecture (number of leaves, mean leaf length, and epiphyte load) were successfully obtained using an underwater photographic technique that was specifically designed to avoid destructive sampling of the seagrass. Results indicated that P. oceanica shoot density was lower than that recorded from the same meadow during a study undertaken in 1995; the observed decrease was attributed to the activities of an offshore aquaculture farm that operated during the period 1995–2000 in the vicinity of the meadow. ANOVA indicated significant spatial and temporal variations in meadow structural attributes at both sites during the 3-year study; for example, shoot density values increased overall with time at site A; a indication of potential recovery of the meadow following cessation of the aquaculture operations. Lower shoot density values recorded from site B (compared with site A) were attributed to higher epiphyte loads on the seagrass, relative to those at site A. The findings, which include new data on the structural characteristics of P. oceanica occurring at depths >40 m, are discussed with reference to the use of the non-destructive photographic technique to monitor the state of health of deep water seagrass meadows.