Food is the largest expense in fish farms. On the other hand, the fish health and wellbeing are determining factors in aquaculture production where nutrition is a vital process for growing animals. In fact, it is important to remember that digestion and nutrition are crucial for animals’ physiology. However, digestion is a very complex process in which food is processed to obtain necessary nutrients and central mechanisms of this process require both endocrine and neuronal regulation. In this context, intestinal motility is essential for the absorption of the nutrients (digestive process determining nutrition). An imbalance in the intestinal motility due to an inadequate diet or an infectious process could result in a lower use of the food and inefficiency in obtaining nutrients from food. Very frequently, farmed fish are infected with different pathogenic microorganism and this situation could alter gastrointestinal physiology and, indirectly reduce fish growth. For these reasons, the present review focuses on analysing how different inflammatory molecules or infections can alter conventional modulators of fish intestinal motility.