Estimating the locations and the structures of subsurface channels holds significant importance for forecasting the subsurface flow and reservoir productivity. These channels exhibit high permeability and are easily contrasted from the low-permeability rock formations in their surroundings. This enables formulating the flow channels estimation problem as a sparse field recovery problem. The ensemble Kalman filter (EnKF) is a widely used technique for the estimation and calibration of subsurface reservoir model parameters, such as permeability. However, the conventional EnKF framework does not provide an efficient mechanism to incorporate prior information on the wide varieties of subsurface geological structures, and often fails to recover and preserve flow channel structures. Recent works in the area of compressed sensing (CS) have shown that estimating in a sparse domain, using algorithms such as the orthogonal matching pursuit (OMP), may significantly improve the estimation quality when dealing with such problems. We propose two new, and computationally efficient, algorithms combining OMP with the EnKF to improve the estimation and recovery of the subsurface geological channels. Numerical experiments suggest that the proposed algorithms provide efficient mechanisms to incorporate and preserve structural information in the EnKF and result in significant improvements in recovering flow channel structures.