Measurement of rates of oxygen consumption ( Mo) in small aquatic embryos or larvae (<1 mm) in response to altered environmental conditions has traditionally been challenging. Here, using modifications of a commercially available fluorescent optode flow-through cell (FTC; PreSens FTC-PSt3) and routine laboratory supplies (syringes, stopcocks, tubing), we have constructed a manual intermittent flow respirometer (MIFR) that allows measurement of Mo in small numbers of individuals when sequentially exposed to different environmental conditions (e.g., changes in seawater pH) through a gravity-driven media replacement perfusion system. We first show that the FTC can be used in "static" mode while incubating small numbers of embryos/larvae contained within the planar oxygen sensor (POS) chamber with Nitex filters. We then demonstrate the use of the MIFR by exposing larval echinoderms ( Fellaster zelandiae, Evechinus chloroticus, and Centrostephanus rodgersii) to seawater equilibrated with elevated CO and measured Mo during acute and chronic exposure to hypercapnia. This MIFR method will allow investigators to address questions regarding the respiratory physiology of small aquatic animals, such as the thresholds for metabolic depression in embryonic and larval forms. NEW & NOTEWORTHY A manual intermittent flow respirometer (MIFR), allowing media exchange in a flow-through cell containing small aquatic organisms, permits repeated measurement of Mo of individuals not only in a single medium (e.g., technical replication), but also in different media (here, high CO-equilibrated seawater), enabling measurement of acute physiological responses to changed conditions. This versatile technique has wide-ranging implications for the study of the Mo response of aquatic organisms in the face of climate change.