Laboratory animals, when subjected to behavioural tests, are often motivationally primed by a period of prior water or food restriction. To date, it is still debatable which restriction protocol (water versus food) is more appropriate for different species. In general, a protocol is considered appropriate if animal discomfort is kept to a minimum whilst motivation for the task is maximised. Here we present a comparison study of the effects of water versus food restriction protocols in mice. The characterisation of the physiological and behavioural effects of food and water restriction in mice is beneficial for both institutional animal care centres and the scientific community. We have investigated body weight fluctuations in three groups of C57BL/6J female mice (water-restricted, food-restricted and control) in two different protocols (20 h versus 22 h of restriction per day) over 2 consecutive weeks. Subsequently, a selected number of mice from each group were subjected to a battery of behavioural tests to investigate exploratory, emotional and dominance behaviours, in addition to learning and memory processes. Body weight fluctuations suggested that mice tolerate a water restriction regimen better than a comparable food restriction regimen. Furthermore, behavioural performances demonstrated that food-restricted mice show a reduction in the exploration of a new environment and particular aspects of their timing memories are distorted. Finally, both water- and food-restricted mice tended to be more offensive than control mice when paired with an opponent in a social dominance test condition.