Management of low-mobility or benthic fisheries is a difficult task because variation in the spatial distribution and population dynamics of the resources make the monitoring and assessment of these fisheries challenging. We assumed that environmental, spatial, and temporal factors can contribute to the variability of the relative abundance of such species; we used Generalized Additive Models for Location Scale and Shape (GAMLSS) to test this hypothesis using as a case study the lobster fishery (targeting two species) in the Galapagos Marine Reserve, Ecuador. We gathered data on each of the two species of lobster on a monthly basis over seven years, including: (a) onboard observers’ records of catch data, fishing effort, and ground location by trip, and (b) data from interviews undertaken with fishers at their arrival to port, recording the same type of information as obtained from onboard observers. We use this information to analyze the effect of the measured variables and to standardize the Catch per Unit Effort (CPUE) in each case, using the GAMLSS. For both species, the temperature, region, fishing schedule, month, distance, and the monitoring system were significant variables of the selected models associated with the variability of the catch rate. For Panulirus penicillatus, CPUE was higher at night than during the day, and for Panulirus gracilis it was higher during the day. Increased temperature resulted in a decrease of CPUE values. It was evident that temporal, spatial scales and monitoring system can influence the variability of this indicator. We contend that the identification of drivers of change of relative abundance in low-mobility species can help to support the development of monitoring and assessment programs for this type of fisheries.