Generalized linear mixed models (GLMMs) are a cornerstone data analysis strategy in behavioral research because of their robustness in handling non-normally distributed variables. Recently, their integration with ordered beta regression (OBR), a novel statistical tool for managing percentage data, has opened new avenues for analyzing continuous response data. Here, we applied this combined approach to investigate nuanced differences between the 3xTg-AD model of Alzheimer’s disease (AD) and their C57BL/6 non-transgenic (NTg) counterparts with normal aging in a 5-day Morris Water Maze (MWM) test protocol. Our longitudinal study included 22 3xTg-AD mice and 15 NTg mice (both male and female) assessed at 12 and 16 months of age. By identifying and analyzing multiple swimming strategies during three different paradigms (cue, place task, and removal), we uncovered genotypic differences in all paradigms. Thus, the NTg group exhibited a higher percentage of direct search behaviors, while an association between circling episodes and 3xTg-AD animals was found. Furthermore, we also propose a novel metric—the “Cognitive Flexibility Index”—which proved sensitive in detecting sex-related differences. Overall, our integrated GLMMs-OBR approach provides a comprehensive insight into mouse behavior in the MWM test, shedding light on the effects of aging and AD pathology.