As you might expect there is no real problem in buying the essentials for baby or toddler in Munich. Rossman, or Tengelmann are two large retailers that have many outlets across Munich. Both have baby sections.
The Apotheke is a chain of German pharmacies found all over the country and also all across Munich. Again they have a comprehensive baby section, they can fill prescriptions from a doctor and they sell over the counter drugs.
Anything else you may need for your baby or toddler can be purchased at a local Galleria. These stores are typically set over five to six stories and can be found in around the centre of Munich.