Crayfish is a very popular aquatic food in many countries, and enrofloxacin (ENR) and ciprofloxacin (CIP) was the most frequently detected in aquatic products. However, limited information is available on the residue characterization, biotransformation rate and withdrawal period (WT) of ENR and CIP in crayfish and health risk via consumption of ENR and CIP remained crayfish. Herein, a comprehensive investigation was conducted to study residue depletion, biotransformation, ingestion risk, and WT of ENR and its predominate metabolite CIP in crayfish following different routes with repeated doses. The results showed that the elimination half-life (T1/2) of target compounds in crayfish were all in order of hepatopancreas > muscle > gill, and the order of T1/2 in different crayfish tissues were intramuscular (IM) route > oral (PO) treatment > immersion (IMMR) administration. The biotransformation rates from ENR to CIP varied from 0.75% to 3.45% in crayfish tissues following different exposure routes. The high dietary risk (RQ > 1) consuming muscle and hepatopancreas of ENR and CIP remained crayfish occurred at early after different administrations. WT is the key to control the drug residue risk, and the longest WT of marker residue of ENR in crayfish was calculated to be 51 d (1275 °C-day).