For negative recharge, the sites represent areas where no recharge takes place or where the net movement of water in the unsaturated zone is vertically upward. This may be a result of several factors such as the local soil composition and the évapotranspiration rate. Also the site may be in a groundwater discharge zone on a microscale and hence the flow may have a vertical component directed upwards.
The basin has an area of 900 km² and the data river flow analised represents this area. I guess this negative recharge is related to water abstraction from river to irrigation in dry periods, but i am looking for some correlated examples in literature.