Cyanobacteria have often been described as nutritionally poor for herbivorous organisms. To gain additional information on the potential impacts of invertebrates feeding on cyanobacteria, we fed Elliptio complanata mussels with two types of algae: Anabaena flos-aquae (cyanobacteria) and Pseudokirchneriella subcapitata (green algae). Physiological parameters were examined at the energy status, immune system and oxidative stress levels. Energy status was examined by following the rate of electron transport activity in mitochondria (a measure of cellular energy expense) and lipid/sugar stores in the visceral mass. The cyanobacteria were not actively producing toxins. Based on the digestive gland index, the mussels fed equally on either regime. However, the energy status in mussels fed A. flos-aquae revealed that the total sugar was lower in the digestive gland, whereas mitochondrial electron transport activity (MET), once corrected against the digestive gland somatic index, showed increased energy expenses. Acetylcholinesterase activity and lipid peroxidation (LPO) were also higher in mussels fed with A. flos-aquae compared with mussels fed with P. subcapitata. LPO was correlated by mitochondrial activity in both the digestive gland and gills, suggesting that oxidative stress resulted from metabolic respiration. Immunocompetence (phagocytic activity, natural killer cell-like activity, haemocyte count and viability) and humoral level of lysozyme were not affected in mussels by the algae or cyanobacteria regime. Moreover, the xenobiotic conjugating enzyme, glutathione S-transferase, hemoprotein oxidase and vitellogenin-like proteins were not affected in mussel organs via ingestion of A. flos-aquae. Our study suggests that ingestion of cyanobacteria leads to increased energy expenses, oxidative stress and increased acetylcholine turnover in mussels.