药房is affiliated to the hospital. 药店is an independent shop.

In my community, 药房 is inside the hospital. It is for the patients to get medicines according to doctors' suggestion. 药店 is the place that you can get normal medicine without doctors' diagnosis. It is outside the hospital. Feel free to ask me if u still have questions.

旧吋中国只有药店一说，没有药房一说。清朝末期西药引进的中国才有了药房，为了区分中西医，卖中药的一般称为中药店的，卖西药的一般称为西药房。不过现在随着改革和竞争的加剧，中西药店都开始卖起了百货和食品。中药店卖西药，西药房也会卖中药，所以它们现在没有太大的区别。In the old days, there were only pharmacies in China, but no pharmacies. In the late qing dynasty, western medicine was introduced into China. In order to distinguish between traditional Chinese medicine and western medicine, those who sold traditional Chinese medicine were generally called Chinese medicine pharmacies, while those who sold western medicine were generally called western medicine pharmacies. But now, as reforms and competition intensify, Chinese and western pharmacies are starting to sell department stores and food. Chinese pharmacies sell western medicine, and western pharmacies also sell Chinese medicine, so there is not much difference between them now.（我是利用翻译软件翻的٩(*´◒`*)۶）

药房: Pharmacies should not only provide accurate and qualified drugs to patients, but also ensure the safe and effective use of drugs by patients, so as to ensure that medical expenses are more economical and reasonable. 药店: A drugstore is a retail store where drugs are sold.

药房 is hospital's pharmacy where hospital dispenses medicines as prescription. 药店 is just pharmacy.