I think to get the best answer you'd need to take it on a case by case basis. Like Jno says, there are stone quarries in the east of the country, but in past times the borders of the Netherlands have changed and so there might also have been further quarries that are now inside Germany or Belgium. However with having well-established sea and river trade links it is very likely that 'quality' stone figured among cargoes for special jobs - marble for church floors, granite for quoins and lintels etc.
There was a well-established trade on hard stone from present-day Germany even before 1000 AD, so it's reasonable to expect stone of different kinds to have been imported.
Up to the architect, really. Think of Portland stone, Aberdeen granite, Mexican and Brazilian onyx, Welsh slate, Italian marble, etc, etc. These have been exported all over the world. The UN building in New York has Portland stone incorporated in its structure, for example.
Many buildings are of brick and timber. For brick you just need clay of course. The majority of the timber came from (would you believe?) the German Black Forest. It was floated down the River Neckar as huge rafts to Mannheim and continued on to Holland along the Rhine. Mark Twain, who was a licenced Mississippi river pilot, actually travelled on one for the last part of the Neckar, a journey outlined in his book 'A Tramp Abroad'.