Here is the location of the organic market in Cuenca https://maps.google.com/maps?q=-2.917025,-79.03067&hl=en&num=1&t=h&z=16
Just tell a taxi driver to take you to “el mercado atras de El Tiempo” El Tiempo is a newspaper. The building is on Av. Loja. Any taxi driver can get you there.
It is open on Sat and Wed from 6AM-noon. Saturday is best. Mostly everything is sold out by 7:30AM so get there early. Wed has much fewer vendors and much less variety of stuff, but what there is last a little longer. Tomatoes are only there on Sat.