Ecological indicators calculated from landings data have been extensively used to evaluate the effects of fishing on marine ecosystems. However, few studies have tested the possible effects of gear and spatial aggregation of landings data on different ecological indices over a long-term period. To do this, we applied the Marine Trophic Index (MTI) and Fishing in Balance (FiB) index to Greek landings data disaggregated by gear and area for the period between 1928 and 2010. Aggregated data showed an increase in MTI due to expansion of fisheries that was also confirmed in most of the disaggregated analysis conducted by fishing subareas and main gear types. On the other hand, disaggregated landings by gear and area provided additional insights: while aggregated landings showed no decline in MTI, disaggregated landings showed that 63% of cases indicated an increase in MTI while 11% showed a decline. When small pelagics and other species were excluded, these values changed to 42% and 24%, respectively. Thus, disaggregated data permitted the identification of ecologically meaningful critical situations with decreasing MTI, as has been observed in shallow enclosed gulfs in close proximity to large cities and/or for the main fishing grounds exploited for long periods by seiners (purse and beach). Moreover, disaggregating landings data by gear increased the ability of explaining observed trends, avoiding masking (averaging) effects and accounting for differential development and adaptability of different gear.