first add this dependency (in addition to mysql-connector-java)

<dependency>
  <groupId>com.vividsolutions</groupId>
  <artifactId>jts</artifactId>
  <version>1.13</version>
</dependency>

and then use following code from http://www.dev-garden.org/2011/11/27/loading-mysql-spatial-data-with-jdbc-and-jts-wkbreader/:

//MySQL geometries are returned in JDBC as binary streams.  The
//stream will be null if the record has no geometry.
try(InputStream inputStream = rs.getBinaryStream("Geom")) {
    Geometry geometry = GeometryParser.getGeometryFromInputStream(inputStream);
}

where rs is a ResultSet (rs = stmt.getResultSet())

, "Geom" is a column of type Geometry, and:

import com.vividsolutions.jts.geom.Geometry;
import com.vividsolutions.jts.io.WKBReader;

import java.io.ByteArrayOutputStream;
import java.io.InputStream;

public class GeometryParser {
    /**
     * http://www.dev-garden.org/2011/11/27/loading-mysql-spatial-data-with-jdbc-and-jts-wkbreader/
     * @param inputStream
     * @return
     * @throws Exception
     */
    public static Geometry getGeometryFromInputStream(InputStream inputStream) throws Exception {

        Geometry dbGeometry = null;

        if (inputStream != null) {

            //convert the stream to a byte[] array
            //so it can be passed to the WKBReader
            byte[] buffer = new byte[255];

            int bytesRead = 0;
            ByteArrayOutputStream baos = new ByteArrayOutputStream();
            while ((bytesRead = inputStream.read(buffer)) != -1) {
                baos.write(buffer, 0, bytesRead);
            }

            byte[] geometryAsBytes = baos.toByteArray();
            baos.close();

            if (geometryAsBytes.length < 5) {
                throw new Exception("Invalid geometry inputStream - less than five bytes");
            }

            //first four bytes of the geometry are the SRID,
            //followed by the actual WKB.  Determine the SRID
            //here
            byte[] sridBytes = new byte[4];
            System.arraycopy(geometryAsBytes, 0, sridBytes, 0, 4);
            boolean bigEndian = (geometryAsBytes[4] == 0x00);

            int srid = 0;
            if (bigEndian) {
                for (int i = 0; i < sridBytes.length; i++) {
                    srid = (srid << 8) + (sridBytes[i] & 0xff);
                }
            } else {
                for (int i = 0; i < sridBytes.length; i++) {
                    srid += (sridBytes[i] & 0xff) << (8 * i);
                }
            }

            //use the JTS WKBReader for WKB parsing
            WKBReader wkbReader = new WKBReader();

            //copy the byte array, removing the first four
            //SRID bytes
            byte[] wkb = new byte[geometryAsBytes.length - 4];
            System.arraycopy(geometryAsBytes, 4, wkb, 0, wkb.length);
            dbGeometry = wkbReader.read(wkb);
            dbGeometry.setSRID(srid);
        }

        return dbGeometry;
    }
}