We retrieved daily cases for all of Spain reported at the level of provinces and the level of Basic Health Areas (BHA) for Catalunya and Madrid (https://doi.org/10.5281/zenodo.4634868). Each record corresponds to a geo-referenced time series where each record has an associated date, the corresponding identifier of the layer, a code of the zone i.e. a province or BHA) and the number of cases reported on that date (daily incidence). Mobility and population data records come from a study conducted by the Spanish Ministry of Transport, Mobility and Urban Agenda (MITMA, \emph{Ministerio de Transportes, Movilidad y Agenda Urbana}) which analyses the mobility and distribution of the population in Spain from February 14th 2020 to May 9th 2021 https://www.mitma.gob.es/ministerio/covid-19/evolucion-movilidad-big-data retrieved from https://doi.org/10.5281/zenodo.4634895. The data records are based on a sample of more than 13 million anonymized mobile-phone lines provided by a single mobile operator whose subscribers are evenly distributed and include two different mobility indicators. Daily origin-destination matrices (ODM) account for the number of trips between 2850 mobility areas that cover almost the entire territory of Spain, reconstructed by combining cell phone antenna coverage areas with districts and municipalities. The second mobility indicator reports for each mobility areas the total number of persons that have performed 0, 1, 2 or more than 2 trips in a given date. The indicator accounts for the fractions of people performing at least one trip or none, as well as the estimated total population in that zone for the given date. In this work, we used the mobility indicators \cite{data-mobility} and population data \cite{data-population}, projected into provinces and BHA. The data set also include the zonifications in geoJSON for zon_bas_13, abs_09 and cnig_provincias retrieved from https://doi.org/10.5281/zenodo.4634663.