The Na⁺/H⁺ exchanger NHE3 associates with the actin cytoskeleton by binding ezrin both directly and indirectly. Both types of interaction are necessary for acute regulation of NHE3. Most acute regulation of NHE3 occurs by changes in trafficking via effects on exocytosis and/or endocytosis. However, NHE3 activity can also be regulated without changing the surface expression of NHE3 (change in turnover number).

A positive amino acid cluster in the a‐helical juxtamembrane region in the COOH‐terminus of NHE3 (amino acids K516, R520 and R527) is necessary for binding to the protein 4.1, ezrin, radixin, moesin (FERM) domain III of ezrin. Direct binding of NHE3 to ezrin is necessary for many aspects of basal trafficking, including basal exocytosis, delivery from the synthetic pathway and movement of NHE3 in the brush border (BB), which probably contributes to endocytosis over a prolonged period of time.

In addition, NHE3 binds indirectly to ezrin. The PDZ domain‐containing proteins Na⁺/H⁺ exchanger regulatory factor (NHERF) 1 and NHERF2, as intermediates in linking NHE3 to ezrin, are necessary for many aspects of NHE3 regulation. The binding of NHERF–ezrin/radixin/moesin to NHE3 occurs in the cytosolic domain of NHE3 between amino acids 475 and 689. This NHERF binding is involved in the formation of the NHE3 complex and restricts NHE3 mobility in the BB. However, it is dynamic; for example, changing in some cases of signalling. Furthermore, NHERF binding is necessary for lysophosphatidic acid stimulation of NHE3 and inhibition of NHE3 by Ca²⁺, cAMP and cGMP.