Director of the Institute: Ing. Yvetta Velísková, PhD.
Deputy Director: Ing. Peter Šurda, PhD.
Scientific secretary: Ing. Renata Dulovičová
Since 2014 the structure of the Institute consists of two scientific departments with two experimental bases:
Department of surface water hydrology (Head: Ing. D. Halmová, PhD.)
Research base for Mountain Hydrology (Head: Ing. M. Danko, PhD.)
Department of subsurface water hydrology (Head: Mgr. Peter Rončák, PhD.)
Research base for Lowland Hydrology (Head: Ing. M. Gomboš, PhD.)
Institute has two organization units:
Department of Scientific-technical information and computer networks (Head: Ing. Ivan Mészároš, PhD.);
Economic and Administrative Department (Head: Ing. Eva Barteková).